Annotations: 6XCN

 6XCN

Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCoronavirus S1 glycoprotein, domain C-like 8092661 3002615 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like 8092473 3002562 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like 8092471 3000282 SCOP2B (2022-06-29)
ASCOP2B SuperfamilySARS coronavirus receptor-binding domain-like 8092467 3001706 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like 8092473 3002562 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus S1 glycoprotein, domain C-like 8092661 3002615 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like 8092471 3000282 SCOP2B (2022-06-29)
B [auth C]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like 8092467 3001706 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilySARS coronavirus receptor-binding domain-like 8092467 3001706 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyCoronavirus spike S2 glycoprotein connector domain-like 8092473 3002562 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyCoronavirus S2 glycoprotein stalk-like 8092471 3000282 SCOP2B (2022-06-29)
C [auth E]SCOP2B SuperfamilyCoronavirus S1 glycoprotein, domain C-like 8092661 3002615 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ASpike_NTDe6xcnA3 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
ASpike_rec_bind_1e6xcnA1 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: Spike_rec_bind_1ECOD (1.6)
ASpike_rec_binde6xcnA2 A: a+b three layersX: Coronavirus spike protein receptor-binding domain (From Homology)H: Coronavirus spike protein receptor-binding domainT: Beta-coronavirus spike protein receptor-binding domainF: Spike_rec_bindECOD (1.6)
ACorona_S2e6xcnA4 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: Corona_S2ECOD (1.6)
B [auth C]Spike_NTDe6xcnC2 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
B [auth C]Spike_rec_bind_1e6xcnC3 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: Spike_rec_bind_1ECOD (1.6)
B [auth C]Spike_rec_binde6xcnC4 A: a+b three layersX: Coronavirus spike protein receptor-binding domain (From Homology)H: Coronavirus spike protein receptor-binding domainT: Beta-coronavirus spike protein receptor-binding domainF: Spike_rec_bindECOD (1.6)
B [auth C]Corona_S2e6xcnC1 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: Corona_S2ECOD (1.6)
C [auth E]Spike_NTDe6xcnE1 A: beta sandwichesX: jelly-rollH: Concanavalin A-likeT: Concanavalin A-like lectins/glucanasesF: Spike_NTDECOD (1.6)
C [auth E]Spike_rec_bind_1e6xcnE2 A: beta complex topologyX: Beta domain of coronavirus spike glycoprotein (From Topology)H: Beta domain of coronavirus spike glycoprotein (From Topology)T: Beta domain of coronavirus spike glycoproteinF: Spike_rec_bind_1ECOD (1.6)
C [auth E]Spike_rec_binde6xcnE3 A: a+b three layersX: Coronavirus spike protein receptor-binding domain (From Homology)H: Coronavirus spike protein receptor-binding domainT: Beta-coronavirus spike protein receptor-binding domainF: Spike_rec_bindECOD (1.6)
C [auth E]Corona_S2e6xcnE4 A: a+b complex topologyX: S2 subunit of coronavirus spike glycoprotein (From Topology)H: S2 subunit of coronavirus spike glycoprotein (From Topology)T: S2 subunit of coronavirus spike glycoproteinF: Corona_S2ECOD (1.6)
D [auth B]V-set_8e6xcnB1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
E [auth F]V-set_8e6xcnF1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
F [auth H]V-set_8e6xcnH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_8ECOD (1.6)
G [auth D]V-set_3e6xcnD1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
H [auth G]V-set_3e6xcnG1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)
I [auth L]V-set_3e6xcnL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: V-set_3ECOD (1.6)

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
D [auth B],
E [auth F],
F [auth H]
Fab C105, anti-SARS-CoV-2, neutralizing VH-CH1 Homo sapiens (human) IGHV3-53*01, IGHJ4*01, IGHJ4*02, IGHJ4*03, IGHJ5*01, IGHJ6-3*01, IGHG1*03, IGHG1*08, IGHG1*06 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_LAMBDA IMGT (202451-0)
G [auth D],
H [auth G],
I [auth L]
Fab C105, anti-SARS-CoV-2, neutralizing L-LAMBDA Homo sapiens (human) IGLV2-8*01, IGLJ2*01, IGLJ3*01, IGLC2*01, IGLC2*02, IGLC3*04 V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA IG FAB-GAMMA-1_LAMBDA IMGT (202451-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
D [auth B],
E [auth F],
F [auth H]
Heavy ChainIGHV3 -spike glycoproteinSAbDab (2024-12-27)
G [auth D],
H [auth G],
I [auth L]
Light ChainIGLV2 Lambdaspike glycoproteinSAbDab (2024-12-27)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A,
B [auth C],
C [auth E]
PF01601Coronavirus spike glycoprotein S2 (CoV_S2)Coronavirus spike glycoprotein S2- Family
A,
B [auth C],
C [auth E]
PF16451Betacoronavirus-like spike glycoprotein S1, N-terminal (bCoV_S1_N)Betacoronavirus-like spike glycoprotein S1, N-terminalThis entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like doma ...Domain
A,
B [auth C],
C [auth E]
PF09408Betacoronavirus spike glycoprotein S1, receptor binding (bCoV_S1_RBD)Betacoronavirus spike glycoprotein S1, receptor bindingThis entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is transla ...Domain
A,
B [auth C],
C [auth E]
PF19209Coronavirus spike glycoprotein S1, C-terminal (CoV_S1_C)Coronavirus spike glycoprotein S1, C-terminalThis entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epide ...Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A,
B [auth C],
C [auth E]
Spike glycoprotein
D [auth B],
E [auth F],
F [auth H]
C105 Fab Heavy Chain---
G [auth D],
H [auth G],
I [auth L]
C105 Fab Light Chain---